/*
 * UniversalClock.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.evomodel.clock;

import dr.inference.model.AbstractModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evolution.tree.Tree;
import dr.evolution.tree.NodeRef;

/**
 * A class that calculates the rate of evolution based on of the mass and temperature
 * @author Alexei Drummond
 * @version $Id: UniversalClock.java,v 1.5 2005/02/21 15:16:09 rambaut Exp $
 */

public class UniversalClock extends AbstractModel implements BranchRateModel {
	
	public static final String UNIVERSAL_CLOCK = "universalClock";	
		
	/**
	 * creates a universal clock model
	 * @param rateParameter the rate vector of *all* nodes
	 * @param massParameter the mass vector of *all* nodes
	 * @param temperatureParameter the temperature vector of *all* nodes 
	 * @param scaleParameter a single-dimensional scale parameter
	 */
	public UniversalClock(
		Parameter rateParameter, 
		Parameter massParameter, 
		Parameter temperatureParameter,
		Parameter scaleParameter	
	) {
		
		super(UNIVERSAL_CLOCK);
		
		this.rateParameter = rateParameter;
		this.massParameter = massParameter;
		this.temperatureParameter = temperatureParameter;
		this.scaleParameter = scaleParameter;
		
		// don't add rate parameter, cause that is what you are changing!
		// you don't care if it changes
		addParameter(massParameter);
		addParameter(temperatureParameter);
		addParameter(scaleParameter);

	}
	
	// *****************************************************************
	// Interface Model
	// *****************************************************************
	
	protected void handleModelChangedEvent(Model model, Object object, int index) {
		// no submodels so nothing to do
	}
	
	protected void handleParameterChangedEvent(Parameter parameter, int index) {
	
		if ((parameter == massParameter) || (parameter == temperatureParameter)) {
			if (index == -1) {
				calculateAllRates();
			} else calculateRate(index);
		} else if (parameter == scaleParameter) {
			calculateAllRates();
		} else {
			throw new RuntimeException("unknown parameter changed in " + UNIVERSAL_CLOCK);
		}
	}
	
	protected void storeState() {} // no additional state needs storing
	protected void restoreState() {} // no additional state needs restoring	
	protected void acceptState() {} // no additional state needs accepting	
		
	/**
	 * Adopt the state of the model component from source.
	 */
	protected void adoptState(Model source) {
		throw new UnsupportedOperationException("this has not been implemented yet");
	}
	
	// **************************************************************
    // Private methods
    // **************************************************************
	
	private void calculateAllRates() {
		int numNodes = massParameter.getDimension();
		for (int i =0; i < numNodes; i++) {
			calculateRate(i);
		}
	}
	
	private void calculateRate(int index) {
	
		double mass = massParameter.getParameterValue(index);
		double temperature = temperatureParameter.getParameterValue(index);
		
		double scale = scaleParameter.getParameterValue(0); 
		
		// replace this with the real equation!!
		double substitutionRate = scale * Math.pow(mass, -0.25) * Math.exp(temperature);
	
		rateParameter.setParameterValue(index, substitutionRate);
	}
	
    public double getBranchRate(Tree tree, NodeRef node) {
        throw new RuntimeException("Look at code before running this class!");
    }

    public String getBranchAttributeLabel() {
        return "rate";
    }

    public String getAttributeForBranch(Tree tree, NodeRef node) {
        return Double.toString(getBranchRate(tree, node));
    }
	
    Parameter rateParameter = null;
	Parameter massParameter = null;
	Parameter temperatureParameter = null;
	Parameter scaleParameter = null;

}

